R: Geographically-Conscious Taxonomic Assignment for Metabarcoding

# Geographically-Conscious Taxonomic Assignment for Metabarcoding

## Documentation for package ‘LocaTT’ version 1.2.0

- DESCRIPTION file
- Package README

## Help Pages

adjust_taxonomies | Adjust Taxonomies
binomial_test | Binomial Test
blast_command_found | Check BLAST Installation
blast_version | Get BLAST Version
circle | Draw Circle Polygon
contains_wildcards | Check Whether DNA Sequences Contain Wildcard Characters
coordinates | Generate Circular Coordinates
decode_quality_scores | Decode DNA Sequence Quality Scores
detection | Grouped Detection Plot
expand_taxonomies | Expand Taxonomies
filter_sequences | Filter DNA Sequences by PCR Replicates
format_reference_database | Format Reference Databases
get_consensus_taxonomy | Get Consensus Taxonomy from Taxonomic Strings
get_taxonomic_level | Get Specified Taxonomic Level from Taxonomic Strings
get_taxonomies.IUCN | Get Taxonomies from IUCN Red List Files
get_taxonomies.species_binomials | Get NCBI Taxonomies from Species Binomials
isolate_amplicon | Trim DNA Sequences to an Amplicon Region Using Forward and Reverse Primer Sequences
local_taxa_tool | Perform Geographically-Conscious Taxonomic Assignment
merge_pairs | Merge Forward and Reverse DNA Sequence Reads
proportion | Grouped Proportion Plot
read.fasta | Read FASTA Files
read.fastq | Read FASTQ Files
reverse_complement | Get the Reverse Complement of a DNA Sequence
sector | Draw Sector Polygon
singular.detection | Singular Detection Plot
singular.proportion | Singular Proportion Plot
substitute_wildcards | Substitute Wildcard Characters in a DNA Sequence
summarize_quality_scores | Summarize Quality Scores
template | Initiate Template Plot
trim_sequences | Trim Target Nucleotide Sequence from DNA Sequences
truncate_and_merge_pairs | Truncate and Merge Forward and Reverse DNA Sequence Reads
truncate_sequences.length | Truncate DNA Sequences to Specified Length
truncate_sequences.probability | Truncate DNA Sequences at Specified Probability that All Bases were Called Correctly
truncate_sequences.quality_score | Truncate DNA Sequences at Specified Quality Score
write.fasta | Write FASTA Files
write.fastq | Write FASTQ Files